Gap junction plaques from rat liver plasma membranes have been subjected to a range of detergent treatments in order to evaluate systematically the influence of different isolation procedures on their structure. The separation of the connexons was found to vary depending on the conditions used. In the absence of detergent the center-to-center separation of the connexons is, on average, approximately 90 A, and they are arranged on a hexagonal lattice so that the symmetry of the double-layered structure approximates to p6m in projection (or p622 in three-dimensions). Exposure to increasing concentration of detergent reduces the connexon separation to values below 80 A. More severe detergent treatment leads to disintegration of the gap junction plaques. Specimens with center-to-center separations smaller than 86 A show progressively larger deviation from p6m symmetry, seen as apparent rotations of the connexon assemblies within the crystal lattice. This reorganization occurs with both ice-embedded and negatively-stained specimens, using ionic or nonionic detergents, and therefore is probably a packing readjustment caused by depletion of intervening lipid molecules.